One of the most important rituals in the Inca Empire was the capacocha. It required the most prestigious sacrificial offering of male and female children and young women who were characterized by their beauty and purity. The aim of this paper is to present the results of a bio-anthropological analysis of the remains of five individuals sacrificed on the summits of Ampato and Pichu Pichu during this ritual. Various methods (bone analysis and radiography) were applied in the investigation due to the diverse states of preservation of the remains. Four individuals were in the same age category: 6–7 years old. The individual Pichu Pichu #2 was sacrificed at age 3.5 years, which makes him the youngest capacocha sacrifice currently known. Results show proper development of the victims’ bodies, the presence of stress markers related to the early childhood period, and, in the case of the Ampato boy, malformation of the cervical vertebrae. The studies of the Pichu Pichu and Ampato sacrifices confirm their widespread origins, privileged position, and high social status. They show that the victims were well-nourished and had proper body growth compared to juveniles from the lower social strata in different cemeteries in the region.